The NID is a different identifier: it's the identifier of the notification, not the alert. The NID is internally matched with the alert so acknowledge using reply is working properly (the NID in the subject line is only a fallback method when matching responses; the primary way is using email message IDs in the reply email).
When the link contains address 0.0.0.0 then you can specify address/hostname to use in the links in the Settings / General Settings / Notification settings.
Thanks for your reply, however the emails I'm sending to acknowledge are not actually acknowledging the alert. I have already used the IP of the server in Notification settings(used 0.0.0.0) for security pupose